Starting phenix.real_space_refine on Fri Mar 6 00:06:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p40_13190/03_2026/7p40_13190_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p40_13190/03_2026/7p40_13190.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7p40_13190/03_2026/7p40_13190_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p40_13190/03_2026/7p40_13190_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7p40_13190/03_2026/7p40_13190.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p40_13190/03_2026/7p40_13190.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 16881 2.51 5 N 4527 2.21 5 O 4926 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26466 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 7064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7064 Classifications: {'peptide': 998} Incomplete info: {'truncation_to_alanine': 244} Link IDs: {'PTRANS': 53, 'TRANS': 944} Chain breaks: 7 Unresolved non-hydrogen bonds: 747 Unresolved non-hydrogen angles: 959 Unresolved non-hydrogen dihedrals: 582 Unresolved non-hydrogen chiralities: 75 Planarities with less than four sites: {'ASP:plan': 25, 'GLU:plan': 17, 'ASN:plan1': 29, 'GLN:plan1': 9, 'PHE:plan': 8, 'ARG:plan': 10, 'TYR:plan': 9, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 437 Chain: "B" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 826 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "C" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 932 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "D" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 826 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "E" Number of atoms: 7064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7064 Classifications: {'peptide': 998} Incomplete info: {'truncation_to_alanine': 244} Link IDs: {'PTRANS': 53, 'TRANS': 944} Chain breaks: 7 Unresolved non-hydrogen bonds: 747 Unresolved non-hydrogen angles: 959 Unresolved non-hydrogen dihedrals: 582 Unresolved non-hydrogen chiralities: 75 Planarities with less than four sites: {'ASP:plan': 25, 'GLU:plan': 17, 'ASN:plan1': 29, 'GLN:plan1': 9, 'PHE:plan': 8, 'ARG:plan': 10, 'TYR:plan': 9, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 437 Chain: "F" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 932 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "G" Number of atoms: 7064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7064 Classifications: {'peptide': 998} Incomplete info: {'truncation_to_alanine': 244} Link IDs: {'PTRANS': 53, 'TRANS': 944} Chain breaks: 7 Unresolved non-hydrogen bonds: 747 Unresolved non-hydrogen angles: 959 Unresolved non-hydrogen dihedrals: 582 Unresolved non-hydrogen chiralities: 75 Planarities with less than four sites: {'ASP:plan': 25, 'GLU:plan': 17, 'ASN:plan1': 29, 'GLN:plan1': 9, 'PHE:plan': 8, 'ARG:plan': 10, 'TYR:plan': 9, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 437 Chain: "H" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 826 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "I" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 932 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Time building chain proxies: 5.51, per 1000 atoms: 0.21 Number of scatterers: 26466 At special positions: 0 Unit cell: (134.48, 132.84, 227.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 132 16.00 O 4926 8.00 N 4527 7.00 C 16881 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 100B" distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.04 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.03 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.03 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.03 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 97 " - pdb=" SG CYS F 100B" distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 166 " distance=2.04 Simple disulfide: pdb=" SG CYS G 291 " - pdb=" SG CYS G 301 " distance=2.03 Simple disulfide: pdb=" SG CYS G 336 " - pdb=" SG CYS G 361 " distance=2.03 Simple disulfide: pdb=" SG CYS G 379 " - pdb=" SG CYS G 432 " distance=2.03 Simple disulfide: pdb=" SG CYS G 391 " - pdb=" SG CYS G 525 " distance=2.03 Simple disulfide: pdb=" SG CYS G 480 " - pdb=" SG CYS G 488 " distance=2.03 Simple disulfide: pdb=" SG CYS G 538 " - pdb=" SG CYS G 590 " distance=2.03 Simple disulfide: pdb=" SG CYS G 617 " - pdb=" SG CYS G 649 " distance=2.03 Simple disulfide: pdb=" SG CYS G 662 " - pdb=" SG CYS G 671 " distance=2.03 Simple disulfide: pdb=" SG CYS G 738 " - pdb=" SG CYS G 760 " distance=2.03 Simple disulfide: pdb=" SG CYS G 743 " - pdb=" SG CYS G 749 " distance=2.03 Simple disulfide: pdb=" SG CYS G1032 " - pdb=" SG CYS G1043 " distance=2.03 Simple disulfide: pdb=" SG CYS G1082 " - pdb=" SG CYS G1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 97 " - pdb=" SG CYS I 100B" distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 1.2 seconds 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6840 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 51 sheets defined 21.3% alpha, 32.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.918A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.530A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.500A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.655A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 967 removed outlier: 3.624A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.134A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 Processing helix chain 'B' and resid 29 through 31 No H-bonds generated for 'chain 'B' and resid 29 through 31' Processing helix chain 'D' and resid 29 through 31 No H-bonds generated for 'chain 'D' and resid 29 through 31' Processing helix chain 'E' and resid 294 through 304 Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 364 through 371 removed outlier: 3.918A pdb=" N LEU E 368 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 390 Processing helix chain 'E' and resid 406 through 410 Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'E' and resid 616 through 620 removed outlier: 3.531A pdb=" N VAL E 620 " --> pdb=" O CYS E 617 " (cutoff:3.500A) Processing helix chain 'E' and resid 737 through 743 Processing helix chain 'E' and resid 746 through 754 Processing helix chain 'E' and resid 755 through 757 No H-bonds generated for 'chain 'E' and resid 755 through 757' Processing helix chain 'E' and resid 758 through 783 removed outlier: 3.500A pdb=" N ASP E 775 " --> pdb=" O ALA E 771 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 825 Processing helix chain 'E' and resid 866 through 885 Processing helix chain 'E' and resid 897 through 909 removed outlier: 3.655A pdb=" N ILE E 909 " --> pdb=" O ARG E 905 " (cutoff:3.500A) Processing helix chain 'E' and resid 913 through 919 Processing helix chain 'E' and resid 919 through 941 Processing helix chain 'E' and resid 945 through 967 removed outlier: 3.626A pdb=" N SER E 967 " --> pdb=" O VAL E 963 " (cutoff:3.500A) Processing helix chain 'E' and resid 976 through 984 Processing helix chain 'E' and resid 985 through 1033 removed outlier: 4.135A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) Processing helix chain 'E' and resid 1140 through 1145 Processing helix chain 'G' and resid 294 through 304 Processing helix chain 'G' and resid 338 through 343 Processing helix chain 'G' and resid 364 through 371 removed outlier: 3.919A pdb=" N LEU G 368 " --> pdb=" O ASP G 364 " (cutoff:3.500A) Processing helix chain 'G' and resid 386 through 390 Processing helix chain 'G' and resid 406 through 410 Processing helix chain 'G' and resid 416 through 422 Processing helix chain 'G' and resid 438 through 443 Processing helix chain 'G' and resid 616 through 620 removed outlier: 3.529A pdb=" N VAL G 620 " --> pdb=" O CYS G 617 " (cutoff:3.500A) Processing helix chain 'G' and resid 737 through 743 Processing helix chain 'G' and resid 746 through 754 Processing helix chain 'G' and resid 755 through 757 No H-bonds generated for 'chain 'G' and resid 755 through 757' Processing helix chain 'G' and resid 758 through 783 removed outlier: 3.501A pdb=" N ASP G 775 " --> pdb=" O ALA G 771 " (cutoff:3.500A) Processing helix chain 'G' and resid 816 through 825 Processing helix chain 'G' and resid 866 through 885 Processing helix chain 'G' and resid 897 through 909 removed outlier: 3.657A pdb=" N ILE G 909 " --> pdb=" O ARG G 905 " (cutoff:3.500A) Processing helix chain 'G' and resid 913 through 919 Processing helix chain 'G' and resid 919 through 941 Processing helix chain 'G' and resid 945 through 967 removed outlier: 3.625A pdb=" N SER G 967 " --> pdb=" O VAL G 963 " (cutoff:3.500A) Processing helix chain 'G' and resid 976 through 984 Processing helix chain 'G' and resid 985 through 1033 removed outlier: 4.134A pdb=" N VAL G 991 " --> pdb=" O PRO G 987 " (cutoff:3.500A) Processing helix chain 'G' and resid 1140 through 1145 Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.259A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.368A pdb=" N PHE A 43 " --> pdb=" O ARG G 567 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ASP G 574 " --> pdb=" O ILE G 587 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLU G 324 " --> pdb=" O ASN G 540 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ASN G 542 " --> pdb=" O GLU G 324 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE G 326 " --> pdb=" O ASN G 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.736A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.787A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 11.297A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.883A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.488A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.425A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 10.217A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.525A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.805A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.211A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.223A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.223A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.503A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.438A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 4 through 6 Processing sheet with id=AB7, first strand: chain 'B' and resid 53 through 54 removed outlier: 6.821A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AB9, first strand: chain 'C' and resid 9 through 12 removed outlier: 3.864A pdb=" N GLY C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.822A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 28 through 30 removed outlier: 8.259A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N SER E 205 " --> pdb=" O PRO E 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 48 through 55 removed outlier: 7.736A pdb=" N THR E 274 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ASP E 290 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU E 276 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA E 288 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LYS E 278 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 84 through 85 removed outlier: 5.788A pdb=" N ARG E 102 " --> pdb=" O ASN E 121 " (cutoff:3.500A) removed outlier: 11.297A pdb=" N VAL E 126 " --> pdb=" O GLU E 169 " (cutoff:3.500A) removed outlier: 9.884A pdb=" N GLU E 169 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 11.488A pdb=" N ILE E 128 " --> pdb=" O THR E 167 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N THR E 167 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N VAL E 130 " --> pdb=" O ASN E 165 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ASN E 165 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N GLU E 132 " --> pdb=" O ALA E 163 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA E 163 " --> pdb=" O GLU E 132 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLN E 134 " --> pdb=" O SER E 161 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL E 159 " --> pdb=" O CYS E 136 " (cutoff:3.500A) removed outlier: 11.423A pdb=" N ASP E 138 " --> pdb=" O PHE E 157 " (cutoff:3.500A) removed outlier: 10.217A pdb=" N PHE E 157 " --> pdb=" O ASP E 138 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 311 through 319 removed outlier: 3.525A pdb=" N THR E 599 " --> pdb=" O GLY E 311 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL E 595 " --> pdb=" O THR E 315 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN E 317 " --> pdb=" O GLY E 593 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N GLY E 593 " --> pdb=" O ASN E 317 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 324 through 328 removed outlier: 6.805A pdb=" N GLU E 324 " --> pdb=" O ASN E 540 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N ASN E 542 " --> pdb=" O GLU E 324 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE E 326 " --> pdb=" O ASN E 542 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 354 through 358 Processing sheet with id=AC9, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'E' and resid 654 through 655 removed outlier: 6.210A pdb=" N ALA E 672 " --> pdb=" O PRO E 665 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 711 through 728 removed outlier: 6.223A pdb=" N GLN E1071 " --> pdb=" O THR E 716 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N PHE E 718 " --> pdb=" O PRO E1069 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE E 720 " --> pdb=" O TYR E1067 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TYR E1067 " --> pdb=" O ILE E 720 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL E 722 " --> pdb=" O VAL E1065 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL E1065 " --> pdb=" O VAL E 722 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR E 724 " --> pdb=" O LEU E1063 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU E1063 " --> pdb=" O THR E 724 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE E 726 " --> pdb=" O VAL E1061 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL E1061 " --> pdb=" O ILE E 726 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLY E1059 " --> pdb=" O PRO E 728 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N GLY E1059 " --> pdb=" O SER E1055 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N SER E1055 " --> pdb=" O GLY E1059 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL E1061 " --> pdb=" O PRO E1053 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU E1063 " --> pdb=" O SER E1051 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N SER E1051 " --> pdb=" O LEU E1063 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL E1065 " --> pdb=" O LEU E1049 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 711 through 728 removed outlier: 6.223A pdb=" N GLN E1071 " --> pdb=" O THR E 716 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N PHE E 718 " --> pdb=" O PRO E1069 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE E 720 " --> pdb=" O TYR E1067 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TYR E1067 " --> pdb=" O ILE E 720 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL E 722 " --> pdb=" O VAL E1065 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL E1065 " --> pdb=" O VAL E 722 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR E 724 " --> pdb=" O LEU E1063 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU E1063 " --> pdb=" O THR E 724 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE E 726 " --> pdb=" O VAL E1061 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL E1061 " --> pdb=" O ILE E 726 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLY E1059 " --> pdb=" O PRO E 728 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 733 through 736 removed outlier: 4.503A pdb=" N LYS E 733 " --> pdb=" O LEU E 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 1120 through 1125 removed outlier: 4.439A pdb=" N ALA E1087 " --> pdb=" O SER E1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 3 through 5 Processing sheet with id=AD8, first strand: chain 'F' and resid 9 through 12 removed outlier: 3.865A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 28 through 30 removed outlier: 8.259A pdb=" N ASN G 61 " --> pdb=" O TYR G 269 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N TYR G 269 " --> pdb=" O ASN G 61 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N SER G 205 " --> pdb=" O PRO G 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 48 through 55 removed outlier: 7.735A pdb=" N THR G 274 " --> pdb=" O ASP G 290 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ASP G 290 " --> pdb=" O THR G 274 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU G 276 " --> pdb=" O ALA G 288 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA G 288 " --> pdb=" O LEU G 276 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LYS G 278 " --> pdb=" O THR G 286 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 84 through 85 removed outlier: 5.788A pdb=" N ARG G 102 " --> pdb=" O ASN G 121 " (cutoff:3.500A) removed outlier: 11.298A pdb=" N VAL G 126 " --> pdb=" O GLU G 169 " (cutoff:3.500A) removed outlier: 9.884A pdb=" N GLU G 169 " --> pdb=" O VAL G 126 " (cutoff:3.500A) removed outlier: 11.490A pdb=" N ILE G 128 " --> pdb=" O THR G 167 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N THR G 167 " --> pdb=" O ILE G 128 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N VAL G 130 " --> pdb=" O ASN G 165 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ASN G 165 " --> pdb=" O VAL G 130 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N GLU G 132 " --> pdb=" O ALA G 163 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA G 163 " --> pdb=" O GLU G 132 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLN G 134 " --> pdb=" O SER G 161 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N VAL G 159 " --> pdb=" O CYS G 136 " (cutoff:3.500A) removed outlier: 11.424A pdb=" N ASP G 138 " --> pdb=" O PHE G 157 " (cutoff:3.500A) removed outlier: 10.217A pdb=" N PHE G 157 " --> pdb=" O ASP G 138 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 311 through 319 removed outlier: 3.525A pdb=" N THR G 599 " --> pdb=" O GLY G 311 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL G 595 " --> pdb=" O THR G 315 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN G 317 " --> pdb=" O GLY G 593 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N GLY G 593 " --> pdb=" O ASN G 317 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLY G 594 " --> pdb=" O GLN G 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 354 through 358 Processing sheet with id=AE5, first strand: chain 'G' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'G' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'G' and resid 654 through 655 removed outlier: 6.210A pdb=" N ALA G 672 " --> pdb=" O PRO G 665 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 711 through 728 removed outlier: 6.223A pdb=" N GLN G1071 " --> pdb=" O THR G 716 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N PHE G 718 " --> pdb=" O PRO G1069 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ILE G 720 " --> pdb=" O TYR G1067 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TYR G1067 " --> pdb=" O ILE G 720 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL G 722 " --> pdb=" O VAL G1065 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL G1065 " --> pdb=" O VAL G 722 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N THR G 724 " --> pdb=" O LEU G1063 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LEU G1063 " --> pdb=" O THR G 724 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE G 726 " --> pdb=" O VAL G1061 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL G1061 " --> pdb=" O ILE G 726 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLY G1059 " --> pdb=" O PRO G 728 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N GLY G1059 " --> pdb=" O SER G1055 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N SER G1055 " --> pdb=" O GLY G1059 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL G1061 " --> pdb=" O PRO G1053 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU G1063 " --> pdb=" O SER G1051 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER G1051 " --> pdb=" O LEU G1063 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL G1065 " --> pdb=" O LEU G1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 711 through 728 removed outlier: 6.223A pdb=" N GLN G1071 " --> pdb=" O THR G 716 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N PHE G 718 " --> pdb=" O PRO G1069 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ILE G 720 " --> pdb=" O TYR G1067 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TYR G1067 " --> pdb=" O ILE G 720 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL G 722 " --> pdb=" O VAL G1065 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL G1065 " --> pdb=" O VAL G 722 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N THR G 724 " --> pdb=" O LEU G1063 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LEU G1063 " --> pdb=" O THR G 724 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE G 726 " --> pdb=" O VAL G1061 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL G1061 " --> pdb=" O ILE G 726 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLY G1059 " --> pdb=" O PRO G 728 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 733 through 736 removed outlier: 4.504A pdb=" N LYS G 733 " --> pdb=" O LEU G 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 1120 through 1125 removed outlier: 4.439A pdb=" N ALA G1087 " --> pdb=" O SER G1123 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AF4, first strand: chain 'H' and resid 53 through 54 removed outlier: 6.821A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 3 through 5 Processing sheet with id=AF6, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.865A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) 1201 hydrogen bonds defined for protein. 3252 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.07 Time building geometry restraints manager: 2.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8681 1.34 - 1.46: 5046 1.46 - 1.58: 13162 1.58 - 1.70: 0 1.70 - 1.81: 168 Bond restraints: 27057 Sorted by residual: bond pdb=" N SER B 94 " pdb=" CA SER B 94 " ideal model delta sigma weight residual 1.459 1.492 -0.032 1.04e-02 9.25e+03 9.73e+00 bond pdb=" N SER D 94 " pdb=" CA SER D 94 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.04e-02 9.25e+03 8.28e+00 bond pdb=" N SER H 94 " pdb=" CA SER H 94 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.04e-02 9.25e+03 8.24e+00 bond pdb=" N SER D 93 " pdb=" CA SER D 93 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.73e+00 bond pdb=" N TRP B 96 " pdb=" CA TRP B 96 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.21e-02 6.83e+03 7.43e+00 ... (remaining 27052 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 36032 1.37 - 2.74: 730 2.74 - 4.11: 156 4.11 - 5.48: 48 5.48 - 6.85: 15 Bond angle restraints: 36981 Sorted by residual: angle pdb=" N GLN B 90 " pdb=" CA GLN B 90 " pdb=" C GLN B 90 " ideal model delta sigma weight residual 109.40 103.77 5.63 1.63e+00 3.76e-01 1.19e+01 angle pdb=" N GLN I 105 " pdb=" CA GLN I 105 " pdb=" C GLN I 105 " ideal model delta sigma weight residual 114.56 110.18 4.38 1.27e+00 6.20e-01 1.19e+01 angle pdb=" N GLN F 105 " pdb=" CA GLN F 105 " pdb=" C GLN F 105 " ideal model delta sigma weight residual 114.56 110.21 4.35 1.27e+00 6.20e-01 1.17e+01 angle pdb=" N GLN D 90 " pdb=" CA GLN D 90 " pdb=" C GLN D 90 " ideal model delta sigma weight residual 109.40 103.84 5.56 1.63e+00 3.76e-01 1.16e+01 angle pdb=" N GLN C 105 " pdb=" CA GLN C 105 " pdb=" C GLN C 105 " ideal model delta sigma weight residual 114.56 110.25 4.31 1.27e+00 6.20e-01 1.15e+01 ... (remaining 36976 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 15039 17.28 - 34.56: 735 34.56 - 51.84: 157 51.84 - 69.12: 47 69.12 - 86.40: 24 Dihedral angle restraints: 16002 sinusoidal: 5367 harmonic: 10635 Sorted by residual: dihedral pdb=" CB CYS E 538 " pdb=" SG CYS E 538 " pdb=" SG CYS E 590 " pdb=" CB CYS E 590 " ideal model delta sinusoidal sigma weight residual -86.00 -152.46 66.46 1 1.00e+01 1.00e-02 5.77e+01 dihedral pdb=" CB CYS G 538 " pdb=" SG CYS G 538 " pdb=" SG CYS G 590 " pdb=" CB CYS G 590 " ideal model delta sinusoidal sigma weight residual -86.00 -152.41 66.41 1 1.00e+01 1.00e-02 5.76e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -152.40 66.40 1 1.00e+01 1.00e-02 5.76e+01 ... (remaining 15999 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3353 0.050 - 0.101: 717 0.101 - 0.151: 199 0.151 - 0.202: 1 0.202 - 0.252: 5 Chirality restraints: 4275 Sorted by residual: chirality pdb=" CB ILE G 101 " pdb=" CA ILE G 101 " pdb=" CG1 ILE G 101 " pdb=" CG2 ILE G 101 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CB ILE A 101 " pdb=" CA ILE A 101 " pdb=" CG1 ILE A 101 " pdb=" CG2 ILE A 101 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CB ILE E 101 " pdb=" CA ILE E 101 " pdb=" CG1 ILE E 101 " pdb=" CG2 ILE E 101 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 4272 not shown) Planarity restraints: 4848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY D 92 " 0.014 2.00e-02 2.50e+03 2.75e-02 7.57e+00 pdb=" C GLY D 92 " -0.048 2.00e-02 2.50e+03 pdb=" O GLY D 92 " 0.018 2.00e-02 2.50e+03 pdb=" N SER D 93 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 92 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.81e+00 pdb=" C GLY B 92 " -0.045 2.00e-02 2.50e+03 pdb=" O GLY B 92 " 0.017 2.00e-02 2.50e+03 pdb=" N SER B 93 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER H 7 " -0.041 5.00e-02 4.00e+02 6.14e-02 6.04e+00 pdb=" N PRO H 8 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO H 8 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO H 8 " -0.034 5.00e-02 4.00e+02 ... (remaining 4845 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3326 2.76 - 3.29: 24629 3.29 - 3.83: 42834 3.83 - 4.36: 47435 4.36 - 4.90: 85811 Nonbonded interactions: 204035 Sorted by model distance: nonbonded pdb=" O GLN E 804 " pdb=" OG SER E 816 " model vdw 2.221 3.040 nonbonded pdb=" O GLN A 804 " pdb=" OG SER A 816 " model vdw 2.222 3.040 nonbonded pdb=" O GLN G 804 " pdb=" OG SER G 816 " model vdw 2.223 3.040 nonbonded pdb=" O GLU G1092 " pdb=" NH1 ARG G1107 " model vdw 2.284 3.120 nonbonded pdb=" O GLU A1092 " pdb=" NH1 ARG A1107 " model vdw 2.284 3.120 ... (remaining 204030 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 23.900 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27105 Z= 0.143 Angle : 0.535 6.847 37077 Z= 0.292 Chirality : 0.045 0.252 4275 Planarity : 0.004 0.061 4848 Dihedral : 11.695 86.401 9018 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.39 % Favored : 96.58 % Rotamer: Outliers : 0.24 % Allowed : 0.16 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.14), residues: 3627 helix: 2.58 (0.20), residues: 690 sheet: 0.84 (0.17), residues: 912 loop : -0.26 (0.14), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 66 TYR 0.016 0.001 TYR H 36 PHE 0.013 0.001 PHE E 906 TRP 0.016 0.002 TRP C 103 HIS 0.002 0.001 HIS G1064 Details of bonding type rmsd covalent geometry : bond 0.00256 (27057) covalent geometry : angle 0.53423 (36981) SS BOND : bond 0.00272 ( 48) SS BOND : angle 0.88657 ( 96) hydrogen bonds : bond 0.12822 ( 1186) hydrogen bonds : angle 6.58431 ( 3252) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 397 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7327 (mtm180) cc_final: 0.6956 (mtm-85) REVERT: A 277 LEU cc_start: 0.8217 (mt) cc_final: 0.8016 (mp) REVERT: A 577 ARG cc_start: 0.7144 (ttm-80) cc_final: 0.6794 (ttm-80) REVERT: A 699 LEU cc_start: 0.8585 (mt) cc_final: 0.8378 (mt) REVERT: C 73 MET cc_start: 0.0367 (mmm) cc_final: -0.2187 (ttm) REVERT: E 423 TYR cc_start: 0.5579 (t80) cc_final: 0.5301 (t80) REVERT: E 741 TYR cc_start: 0.8913 (t80) cc_final: 0.8506 (t80) REVERT: E 902 MET cc_start: 0.7256 (tpp) cc_final: 0.6908 (mmm) REVERT: F 59 TYR cc_start: 0.3733 (m-80) cc_final: 0.3357 (m-80) REVERT: F 80 MET cc_start: 0.2189 (ppp) cc_final: 0.0030 (tmm) REVERT: G 274 THR cc_start: 0.8512 (m) cc_final: 0.8282 (p) REVERT: G 731 MET cc_start: 0.7374 (ptm) cc_final: 0.7112 (ptm) REVERT: G 742 ILE cc_start: 0.8933 (mt) cc_final: 0.8587 (mt) REVERT: G 1047 TYR cc_start: 0.8242 (m-80) cc_final: 0.7902 (m-10) outliers start: 6 outliers final: 0 residues processed: 403 average time/residue: 0.1474 time to fit residues: 97.3629 Evaluate side-chains 226 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.1980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN A1071 GLN E 218 GLN E 321 GLN F 96 ASN G 207 HIS G1010 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.184554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.122720 restraints weight = 53254.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.127333 restraints weight = 24615.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.128708 restraints weight = 16154.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.130237 restraints weight = 11328.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.130643 restraints weight = 9040.737| |-----------------------------------------------------------------------------| r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 27105 Z= 0.119 Angle : 0.540 10.007 37077 Z= 0.278 Chirality : 0.045 0.205 4275 Planarity : 0.004 0.050 4848 Dihedral : 3.632 18.121 3900 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.85 % Allowed : 7.45 % Favored : 91.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.14), residues: 3627 helix: 2.67 (0.20), residues: 660 sheet: 0.97 (0.17), residues: 894 loop : -0.24 (0.14), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 237 TYR 0.026 0.001 TYR C 79 PHE 0.021 0.001 PHE E 92 TRP 0.035 0.001 TRP F 47 HIS 0.006 0.001 HIS G 207 Details of bonding type rmsd covalent geometry : bond 0.00265 (27057) covalent geometry : angle 0.53825 (36981) SS BOND : bond 0.00321 ( 48) SS BOND : angle 1.09849 ( 96) hydrogen bonds : bond 0.03727 ( 1186) hydrogen bonds : angle 5.55325 ( 3252) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 238 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7610 (mtm180) cc_final: 0.7294 (mtm110) REVERT: A 577 ARG cc_start: 0.7356 (ttm-80) cc_final: 0.7123 (ttm170) REVERT: A 699 LEU cc_start: 0.8891 (mt) cc_final: 0.8623 (mt) REVERT: A 900 MET cc_start: 0.6515 (mtm) cc_final: 0.6046 (mtm) REVERT: C 2 MET cc_start: 0.4735 (mmt) cc_final: 0.4257 (mmt) REVERT: C 5 VAL cc_start: 0.6451 (t) cc_final: 0.6110 (m) REVERT: C 73 MET cc_start: 0.2236 (mmm) cc_final: -0.1088 (ttm) REVERT: C 77 THR cc_start: 0.4924 (OUTLIER) cc_final: 0.3919 (t) REVERT: E 92 PHE cc_start: 0.7042 (t80) cc_final: 0.6800 (t80) REVERT: E 237 ARG cc_start: 0.6816 (ptm-80) cc_final: 0.6279 (ptm-80) REVERT: E 423 TYR cc_start: 0.6737 (t80) cc_final: 0.6336 (t80) REVERT: E 741 TYR cc_start: 0.9213 (t80) cc_final: 0.8670 (t80) REVERT: E 873 TYR cc_start: 0.8022 (m-80) cc_final: 0.7762 (m-80) REVERT: F 59 TYR cc_start: 0.4486 (m-80) cc_final: 0.2983 (m-10) REVERT: F 80 MET cc_start: 0.1906 (ppp) cc_final: 0.0153 (tmm) REVERT: G 237 ARG cc_start: 0.7715 (mtm110) cc_final: 0.7377 (mtm180) REVERT: G 571 ASP cc_start: 0.6969 (t0) cc_final: 0.6722 (t0) REVERT: G 759 PHE cc_start: 0.6614 (OUTLIER) cc_final: 0.6345 (t80) REVERT: G 961 THR cc_start: 0.8882 (m) cc_final: 0.8662 (p) REVERT: G 1047 TYR cc_start: 0.8418 (m-80) cc_final: 0.8064 (m-10) REVERT: H 47 LEU cc_start: 0.4619 (tp) cc_final: 0.4108 (mt) outliers start: 21 outliers final: 13 residues processed: 252 average time/residue: 0.1387 time to fit residues: 58.8423 Evaluate side-chains 214 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 199 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain E residue 533 LEU Chi-restraints excluded: chain G residue 207 HIS Chi-restraints excluded: chain G residue 533 LEU Chi-restraints excluded: chain G residue 721 SER Chi-restraints excluded: chain G residue 759 PHE Chi-restraints excluded: chain G residue 791 THR Chi-restraints excluded: chain G residue 1116 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 111 optimal weight: 20.0000 chunk 90 optimal weight: 0.8980 chunk 256 optimal weight: 20.0000 chunk 88 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 chunk 358 optimal weight: 20.0000 chunk 38 optimal weight: 8.9990 chunk 180 optimal weight: 7.9990 chunk 197 optimal weight: 0.2980 chunk 76 optimal weight: 0.3980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 901 GLN G1010 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.182945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.122179 restraints weight = 52705.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.125684 restraints weight = 28957.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.125198 restraints weight = 16517.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.125815 restraints weight = 16625.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.126044 restraints weight = 14955.758| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 27105 Z= 0.118 Angle : 0.516 10.484 37077 Z= 0.264 Chirality : 0.045 0.184 4275 Planarity : 0.004 0.061 4848 Dihedral : 3.533 15.778 3900 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.22 % Allowed : 9.19 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.14), residues: 3627 helix: 2.53 (0.20), residues: 663 sheet: 0.87 (0.17), residues: 912 loop : -0.25 (0.14), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 815 TYR 0.021 0.001 TYR B 49 PHE 0.024 0.001 PHE E 338 TRP 0.025 0.001 TRP C 50 HIS 0.016 0.001 HIS G 207 Details of bonding type rmsd covalent geometry : bond 0.00267 (27057) covalent geometry : angle 0.51424 (36981) SS BOND : bond 0.00387 ( 48) SS BOND : angle 1.02680 ( 96) hydrogen bonds : bond 0.03625 ( 1186) hydrogen bonds : angle 5.31543 ( 3252) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 225 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.8542 (tp) cc_final: 0.8137 (tp) REVERT: A 338 PHE cc_start: 0.8001 (m-10) cc_final: 0.7717 (m-10) REVERT: A 577 ARG cc_start: 0.7493 (ttm-80) cc_final: 0.7111 (ttm-80) REVERT: A 699 LEU cc_start: 0.8971 (mt) cc_final: 0.8711 (mt) REVERT: A 970 PHE cc_start: 0.7965 (m-10) cc_final: 0.7549 (m-10) REVERT: A 1047 TYR cc_start: 0.8573 (m-80) cc_final: 0.8100 (m-80) REVERT: C 2 MET cc_start: 0.5298 (mmt) cc_final: 0.4346 (mmt) REVERT: C 23 LYS cc_start: 0.7249 (mttp) cc_final: 0.6616 (ttpp) REVERT: C 73 MET cc_start: 0.2400 (mmm) cc_final: -0.1040 (ttm) REVERT: C 108 MET cc_start: 0.0676 (mpp) cc_final: -0.0755 (mmt) REVERT: E 237 ARG cc_start: 0.6731 (ptm-80) cc_final: 0.6116 (ptm-80) REVERT: E 423 TYR cc_start: 0.7078 (t80) cc_final: 0.6820 (t80) REVERT: E 873 TYR cc_start: 0.8053 (m-80) cc_final: 0.7778 (m-80) REVERT: E 902 MET cc_start: 0.7784 (mmm) cc_final: 0.7516 (mmm) REVERT: F 59 TYR cc_start: 0.4842 (m-80) cc_final: 0.3121 (m-80) REVERT: F 80 MET cc_start: 0.1757 (ppp) cc_final: -0.0056 (tmm) REVERT: G 237 ARG cc_start: 0.7565 (mtm110) cc_final: 0.7157 (mtm180) REVERT: G 392 PHE cc_start: 0.6939 (m-80) cc_final: 0.6663 (m-10) REVERT: G 515 PHE cc_start: 0.7542 (m-80) cc_final: 0.7244 (m-10) REVERT: G 537 LYS cc_start: 0.8589 (ttpp) cc_final: 0.8032 (ttpt) REVERT: G 571 ASP cc_start: 0.7185 (t0) cc_final: 0.6968 (t0) REVERT: G 586 ASP cc_start: 0.6577 (t70) cc_final: 0.6276 (t0) REVERT: G 697 MET cc_start: 0.8265 (mtm) cc_final: 0.8008 (mtm) REVERT: G 902 MET cc_start: 0.8319 (mmm) cc_final: 0.8086 (mmm) REVERT: G 1047 TYR cc_start: 0.8456 (m-80) cc_final: 0.8140 (m-10) REVERT: H 47 LEU cc_start: 0.4631 (tp) cc_final: 0.4133 (mt) outliers start: 30 outliers final: 17 residues processed: 247 average time/residue: 0.1439 time to fit residues: 60.2786 Evaluate side-chains 210 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 193 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain E residue 533 LEU Chi-restraints excluded: chain G residue 538 CYS Chi-restraints excluded: chain G residue 560 LEU Chi-restraints excluded: chain G residue 721 SER Chi-restraints excluded: chain G residue 791 THR Chi-restraints excluded: chain G residue 1116 THR Chi-restraints excluded: chain I residue 87 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 62 optimal weight: 0.9980 chunk 265 optimal weight: 0.7980 chunk 268 optimal weight: 50.0000 chunk 288 optimal weight: 8.9990 chunk 72 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 170 optimal weight: 20.0000 chunk 234 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 251 optimal weight: 7.9990 chunk 266 optimal weight: 4.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 207 HIS G 762 GLN G 907 ASN I 96 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.182393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.124232 restraints weight = 53305.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.125085 restraints weight = 34321.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.124125 restraints weight = 21733.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.125034 restraints weight = 22088.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.125834 restraints weight = 18108.587| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 27105 Z= 0.192 Angle : 0.571 9.659 37077 Z= 0.296 Chirality : 0.046 0.165 4275 Planarity : 0.004 0.051 4848 Dihedral : 3.805 15.846 3900 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.19 % Allowed : 10.37 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.14), residues: 3627 helix: 2.19 (0.20), residues: 675 sheet: 0.91 (0.17), residues: 885 loop : -0.41 (0.14), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 66 TYR 0.017 0.002 TYR C 79 PHE 0.023 0.002 PHE E 898 TRP 0.020 0.001 TRP F 50 HIS 0.008 0.001 HIS G1064 Details of bonding type rmsd covalent geometry : bond 0.00447 (27057) covalent geometry : angle 0.56879 (36981) SS BOND : bond 0.00404 ( 48) SS BOND : angle 1.16864 ( 96) hydrogen bonds : bond 0.04201 ( 1186) hydrogen bonds : angle 5.47420 ( 3252) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 215 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.8576 (tp) cc_final: 0.8242 (tp) REVERT: A 237 ARG cc_start: 0.7388 (mtm180) cc_final: 0.6862 (ttp-110) REVERT: A 275 PHE cc_start: 0.7955 (m-80) cc_final: 0.7522 (m-10) REVERT: A 577 ARG cc_start: 0.7699 (ttm-80) cc_final: 0.7171 (ttm-80) REVERT: A 699 LEU cc_start: 0.9098 (mt) cc_final: 0.8797 (mt) REVERT: A 970 PHE cc_start: 0.8453 (m-10) cc_final: 0.8054 (m-10) REVERT: C 2 MET cc_start: 0.5379 (mmt) cc_final: 0.4603 (mmt) REVERT: C 23 LYS cc_start: 0.7424 (mttp) cc_final: 0.6898 (ttpp) REVERT: C 73 MET cc_start: 0.1975 (mmm) cc_final: -0.1342 (ttm) REVERT: C 108 MET cc_start: 0.1769 (mpp) cc_final: -0.0355 (mmt) REVERT: E 223 LEU cc_start: 0.7771 (mp) cc_final: 0.7496 (mt) REVERT: E 237 ARG cc_start: 0.6831 (ptm-80) cc_final: 0.6197 (ptm-80) REVERT: E 275 PHE cc_start: 0.7980 (m-80) cc_final: 0.7724 (m-10) REVERT: E 400 PHE cc_start: 0.7739 (p90) cc_final: 0.6655 (p90) REVERT: E 421 TYR cc_start: 0.7714 (m-80) cc_final: 0.7502 (m-10) REVERT: E 423 TYR cc_start: 0.6761 (t80) cc_final: 0.6237 (t80) REVERT: E 873 TYR cc_start: 0.8023 (m-10) cc_final: 0.7745 (m-80) REVERT: E 902 MET cc_start: 0.8257 (mmm) cc_final: 0.7840 (mmm) REVERT: F 80 MET cc_start: 0.1122 (ppp) cc_final: -0.0569 (tmm) REVERT: G 237 ARG cc_start: 0.7701 (mtm110) cc_final: 0.7248 (mtm180) REVERT: G 338 PHE cc_start: 0.7055 (m-10) cc_final: 0.6830 (m-80) REVERT: G 392 PHE cc_start: 0.7032 (m-80) cc_final: 0.6712 (m-10) REVERT: G 515 PHE cc_start: 0.7628 (m-80) cc_final: 0.7376 (m-10) REVERT: G 571 ASP cc_start: 0.7399 (t0) cc_final: 0.7106 (t0) REVERT: G 586 ASP cc_start: 0.6623 (t70) cc_final: 0.6310 (t0) REVERT: G 724 THR cc_start: 0.9135 (m) cc_final: 0.8929 (p) REVERT: G 902 MET cc_start: 0.8645 (mmm) cc_final: 0.8333 (mmm) REVERT: G 1047 TYR cc_start: 0.8355 (m-80) cc_final: 0.8030 (m-10) REVERT: H 47 LEU cc_start: 0.4945 (tp) cc_final: 0.4452 (mt) REVERT: I 2 MET cc_start: 0.3543 (pmm) cc_final: 0.2878 (pmm) outliers start: 54 outliers final: 29 residues processed: 257 average time/residue: 0.1460 time to fit residues: 63.6922 Evaluate side-chains 216 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 533 LEU Chi-restraints excluded: chain E residue 736 VAL Chi-restraints excluded: chain E residue 1001 LEU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain G residue 200 TYR Chi-restraints excluded: chain G residue 538 CYS Chi-restraints excluded: chain G residue 560 LEU Chi-restraints excluded: chain G residue 721 SER Chi-restraints excluded: chain G residue 791 THR Chi-restraints excluded: chain G residue 900 MET Chi-restraints excluded: chain G residue 907 ASN Chi-restraints excluded: chain G residue 1104 VAL Chi-restraints excluded: chain G residue 1116 THR Chi-restraints excluded: chain G residue 1125 ASN Chi-restraints excluded: chain I residue 87 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 201 optimal weight: 1.9990 chunk 300 optimal weight: 0.9990 chunk 315 optimal weight: 1.9990 chunk 304 optimal weight: 0.8980 chunk 255 optimal weight: 4.9990 chunk 141 optimal weight: 0.0040 chunk 344 optimal weight: 7.9990 chunk 126 optimal weight: 30.0000 chunk 239 optimal weight: 10.0000 chunk 263 optimal weight: 5.9990 chunk 339 optimal weight: 8.9990 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN B 37 GLN I 96 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.178623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.115651 restraints weight = 52263.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.119821 restraints weight = 26568.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.120815 restraints weight = 15435.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.121579 restraints weight = 13787.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.121517 restraints weight = 11983.880| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 27105 Z= 0.141 Angle : 0.545 10.585 37077 Z= 0.276 Chirality : 0.045 0.191 4275 Planarity : 0.004 0.058 4848 Dihedral : 3.682 15.292 3900 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.82 % Allowed : 11.79 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.14), residues: 3627 helix: 1.97 (0.20), residues: 696 sheet: 0.85 (0.17), residues: 888 loop : -0.35 (0.14), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 815 TYR 0.015 0.001 TYR C 79 PHE 0.029 0.002 PHE G 168 TRP 0.022 0.001 TRP B 96 HIS 0.003 0.001 HIS G1064 Details of bonding type rmsd covalent geometry : bond 0.00327 (27057) covalent geometry : angle 0.54031 (36981) SS BOND : bond 0.00424 ( 48) SS BOND : angle 1.44745 ( 96) hydrogen bonds : bond 0.03853 ( 1186) hydrogen bonds : angle 5.36386 ( 3252) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 202 time to evaluate : 0.695 Fit side-chains revert: symmetry clash REVERT: A 189 LEU cc_start: 0.8611 (tp) cc_final: 0.8281 (tp) REVERT: A 906 PHE cc_start: 0.8686 (OUTLIER) cc_final: 0.7034 (m-10) REVERT: A 970 PHE cc_start: 0.8593 (m-80) cc_final: 0.8223 (m-10) REVERT: C 2 MET cc_start: 0.5341 (mmt) cc_final: 0.4611 (mmt) REVERT: C 23 LYS cc_start: 0.7326 (mttp) cc_final: 0.6892 (ttpp) REVERT: C 65 GLU cc_start: 0.3407 (OUTLIER) cc_final: 0.2697 (pp20) REVERT: C 73 MET cc_start: 0.2191 (mmm) cc_final: -0.1102 (ttm) REVERT: C 108 MET cc_start: 0.1594 (mpp) cc_final: -0.0300 (mmt) REVERT: E 223 LEU cc_start: 0.7484 (mp) cc_final: 0.7198 (mt) REVERT: E 275 PHE cc_start: 0.7868 (m-80) cc_final: 0.7635 (m-10) REVERT: E 400 PHE cc_start: 0.7683 (p90) cc_final: 0.6656 (p90) REVERT: E 423 TYR cc_start: 0.6810 (t80) cc_final: 0.6273 (t80) REVERT: E 902 MET cc_start: 0.7970 (mmm) cc_final: 0.7512 (mmm) REVERT: F 2 MET cc_start: 0.1244 (ptt) cc_final: 0.0260 (mpp) REVERT: F 59 TYR cc_start: 0.6964 (m-80) cc_final: 0.6741 (t80) REVERT: F 65 GLU cc_start: 0.0539 (OUTLIER) cc_final: 0.0226 (pm20) REVERT: F 80 MET cc_start: 0.1136 (ppp) cc_final: -0.0431 (tmm) REVERT: G 117 LEU cc_start: 0.8155 (mt) cc_final: 0.7741 (tp) REVERT: G 237 ARG cc_start: 0.7605 (mtm110) cc_final: 0.7313 (mtp-110) REVERT: G 392 PHE cc_start: 0.7215 (m-80) cc_final: 0.6858 (m-10) REVERT: G 515 PHE cc_start: 0.7752 (m-80) cc_final: 0.7481 (m-80) REVERT: G 571 ASP cc_start: 0.7289 (t0) cc_final: 0.7075 (t0) REVERT: G 586 ASP cc_start: 0.7110 (t70) cc_final: 0.6839 (t0) REVERT: G 724 THR cc_start: 0.9085 (m) cc_final: 0.8863 (p) REVERT: G 902 MET cc_start: 0.8700 (mmm) cc_final: 0.8345 (mmm) REVERT: G 1047 TYR cc_start: 0.8366 (m-80) cc_final: 0.8022 (m-10) REVERT: H 47 LEU cc_start: 0.4971 (tp) cc_final: 0.4464 (mt) REVERT: I 2 MET cc_start: 0.3038 (pmm) cc_final: 0.2754 (pmm) outliers start: 45 outliers final: 28 residues processed: 240 average time/residue: 0.1337 time to fit residues: 55.1713 Evaluate side-chains 215 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 184 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain E residue 736 VAL Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain F residue 50 TRP Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain G residue 538 CYS Chi-restraints excluded: chain G residue 560 LEU Chi-restraints excluded: chain G residue 721 SER Chi-restraints excluded: chain G residue 791 THR Chi-restraints excluded: chain G residue 900 MET Chi-restraints excluded: chain G residue 1096 VAL Chi-restraints excluded: chain G residue 1104 VAL Chi-restraints excluded: chain G residue 1116 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 41 optimal weight: 50.0000 chunk 67 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 chunk 194 optimal weight: 1.9990 chunk 332 optimal weight: 0.9990 chunk 139 optimal weight: 9.9990 chunk 40 optimal weight: 8.9990 chunk 298 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 chunk 354 optimal weight: 6.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 GLN B 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.178623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.116893 restraints weight = 52623.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.120229 restraints weight = 28538.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.120724 restraints weight = 17682.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.121412 restraints weight = 14502.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.121818 restraints weight = 13838.645| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 27105 Z= 0.153 Angle : 0.547 10.205 37077 Z= 0.278 Chirality : 0.045 0.149 4275 Planarity : 0.004 0.055 4848 Dihedral : 3.686 15.487 3900 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.07 % Allowed : 12.35 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.14), residues: 3627 helix: 2.17 (0.20), residues: 672 sheet: 0.83 (0.17), residues: 888 loop : -0.36 (0.14), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 577 TYR 0.030 0.001 TYR G 904 PHE 0.025 0.002 PHE E 92 TRP 0.020 0.001 TRP C 50 HIS 0.004 0.001 HIS E1064 Details of bonding type rmsd covalent geometry : bond 0.00354 (27057) covalent geometry : angle 0.54379 (36981) SS BOND : bond 0.00377 ( 48) SS BOND : angle 1.30033 ( 96) hydrogen bonds : bond 0.03876 ( 1186) hydrogen bonds : angle 5.29721 ( 3252) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 201 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.8529 (tp) cc_final: 0.8170 (tp) REVERT: A 515 PHE cc_start: 0.7417 (m-80) cc_final: 0.7182 (m-80) REVERT: A 970 PHE cc_start: 0.8656 (m-80) cc_final: 0.8320 (m-10) REVERT: C 2 MET cc_start: 0.5572 (mmt) cc_final: 0.4842 (mmt) REVERT: C 23 LYS cc_start: 0.7306 (mttp) cc_final: 0.6899 (ttpp) REVERT: C 65 GLU cc_start: 0.3827 (OUTLIER) cc_final: 0.2761 (pp20) REVERT: C 73 MET cc_start: 0.2108 (mmm) cc_final: -0.1102 (ttm) REVERT: C 108 MET cc_start: 0.1643 (mpp) cc_final: -0.0261 (mmt) REVERT: E 237 ARG cc_start: 0.7394 (ptt-90) cc_final: 0.6916 (ptt-90) REVERT: E 275 PHE cc_start: 0.7907 (m-80) cc_final: 0.7609 (m-10) REVERT: E 400 PHE cc_start: 0.7677 (p90) cc_final: 0.6689 (p90) REVERT: E 423 TYR cc_start: 0.6865 (t80) cc_final: 0.6366 (t80) REVERT: E 675 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7550 (pp30) REVERT: E 732 THR cc_start: 0.8496 (m) cc_final: 0.8255 (p) REVERT: E 820 ASP cc_start: 0.7737 (t70) cc_final: 0.7277 (t0) REVERT: E 902 MET cc_start: 0.8030 (mmm) cc_final: 0.7529 (mmm) REVERT: F 2 MET cc_start: 0.1244 (ptt) cc_final: 0.0198 (mpp) REVERT: F 65 GLU cc_start: 0.0621 (OUTLIER) cc_final: 0.0306 (pm20) REVERT: F 80 MET cc_start: 0.1093 (ppp) cc_final: -0.0372 (tmm) REVERT: G 117 LEU cc_start: 0.8086 (mt) cc_final: 0.7711 (tp) REVERT: G 237 ARG cc_start: 0.7644 (mtm110) cc_final: 0.7340 (mtp-110) REVERT: G 240 THR cc_start: 0.7229 (p) cc_final: 0.6974 (t) REVERT: G 392 PHE cc_start: 0.7299 (m-80) cc_final: 0.6817 (m-10) REVERT: G 515 PHE cc_start: 0.7849 (m-80) cc_final: 0.7566 (m-80) REVERT: G 571 ASP cc_start: 0.7314 (t0) cc_final: 0.7096 (t0) REVERT: G 586 ASP cc_start: 0.7191 (t70) cc_final: 0.6942 (t0) REVERT: G 675 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7634 (tm-30) REVERT: G 724 THR cc_start: 0.9107 (m) cc_final: 0.8886 (p) REVERT: G 732 THR cc_start: 0.8669 (m) cc_final: 0.8425 (p) REVERT: G 902 MET cc_start: 0.8730 (mmm) cc_final: 0.8354 (mmm) REVERT: G 1047 TYR cc_start: 0.8379 (m-80) cc_final: 0.8083 (m-10) REVERT: H 47 LEU cc_start: 0.5339 (tp) cc_final: 0.4893 (mt) outliers start: 51 outliers final: 32 residues processed: 239 average time/residue: 0.1398 time to fit residues: 56.8913 Evaluate side-chains 217 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 181 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain E residue 675 GLN Chi-restraints excluded: chain E residue 736 VAL Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain E residue 1010 GLN Chi-restraints excluded: chain F residue 50 TRP Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain G residue 200 TYR Chi-restraints excluded: chain G residue 538 CYS Chi-restraints excluded: chain G residue 560 LEU Chi-restraints excluded: chain G residue 675 GLN Chi-restraints excluded: chain G residue 721 SER Chi-restraints excluded: chain G residue 791 THR Chi-restraints excluded: chain G residue 869 MET Chi-restraints excluded: chain G residue 900 MET Chi-restraints excluded: chain G residue 1096 VAL Chi-restraints excluded: chain G residue 1104 VAL Chi-restraints excluded: chain G residue 1116 THR Chi-restraints excluded: chain I residue 87 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 90 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 227 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 209 optimal weight: 1.9990 chunk 345 optimal weight: 6.9990 chunk 212 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 193 optimal weight: 0.9980 chunk 355 optimal weight: 30.0000 chunk 178 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.175541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.116840 restraints weight = 52332.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.116174 restraints weight = 36503.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.116350 restraints weight = 26348.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.117237 restraints weight = 23564.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.117733 restraints weight = 19443.928| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 27105 Z= 0.210 Angle : 0.591 10.492 37077 Z= 0.304 Chirality : 0.047 0.307 4275 Planarity : 0.004 0.049 4848 Dihedral : 3.907 16.416 3900 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.07 % Allowed : 13.08 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.14), residues: 3627 helix: 2.00 (0.20), residues: 672 sheet: 0.65 (0.17), residues: 924 loop : -0.48 (0.14), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 815 TYR 0.046 0.002 TYR G 904 PHE 0.025 0.002 PHE A 238 TRP 0.017 0.001 TRP C 50 HIS 0.006 0.001 HIS E1064 Details of bonding type rmsd covalent geometry : bond 0.00491 (27057) covalent geometry : angle 0.58830 (36981) SS BOND : bond 0.00458 ( 48) SS BOND : angle 1.31531 ( 96) hydrogen bonds : bond 0.04332 ( 1186) hydrogen bonds : angle 5.44954 ( 3252) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 193 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: A 131 CYS cc_start: 0.2262 (m) cc_final: 0.1154 (m) REVERT: A 189 LEU cc_start: 0.8320 (tp) cc_final: 0.8044 (tp) REVERT: A 241 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.6656 (mm) REVERT: A 275 PHE cc_start: 0.7834 (m-80) cc_final: 0.7509 (m-10) REVERT: A 338 PHE cc_start: 0.8076 (m-10) cc_final: 0.7623 (m-80) REVERT: A 1047 TYR cc_start: 0.8731 (m-80) cc_final: 0.8407 (m-80) REVERT: C 2 MET cc_start: 0.5292 (mmt) cc_final: 0.4646 (mmt) REVERT: C 23 LYS cc_start: 0.6948 (mttp) cc_final: 0.6600 (ttpp) REVERT: C 46 GLU cc_start: 0.0329 (OUTLIER) cc_final: -0.0167 (pp20) REVERT: C 108 MET cc_start: 0.2464 (mpp) cc_final: 0.0647 (mmt) REVERT: E 237 ARG cc_start: 0.7455 (ptt-90) cc_final: 0.7008 (ptt-90) REVERT: E 275 PHE cc_start: 0.8033 (m-80) cc_final: 0.7818 (m-10) REVERT: E 400 PHE cc_start: 0.7807 (p90) cc_final: 0.6812 (p90) REVERT: E 423 TYR cc_start: 0.6891 (t80) cc_final: 0.6395 (t80) REVERT: E 732 THR cc_start: 0.8389 (m) cc_final: 0.8144 (p) REVERT: E 820 ASP cc_start: 0.7904 (t70) cc_final: 0.7503 (t0) REVERT: E 902 MET cc_start: 0.8327 (mmm) cc_final: 0.7784 (mmm) REVERT: E 904 TYR cc_start: 0.7923 (m-10) cc_final: 0.7629 (m-10) REVERT: F 2 MET cc_start: 0.0982 (ptt) cc_final: 0.0686 (mpp) REVERT: F 46 GLU cc_start: 0.1948 (OUTLIER) cc_final: 0.1111 (pm20) REVERT: F 65 GLU cc_start: 0.0837 (OUTLIER) cc_final: 0.0519 (pm20) REVERT: F 80 MET cc_start: 0.1026 (ppp) cc_final: -0.0247 (tmm) REVERT: G 117 LEU cc_start: 0.8221 (mt) cc_final: 0.7859 (tp) REVERT: G 237 ARG cc_start: 0.7697 (mtm110) cc_final: 0.7198 (mtm180) REVERT: G 392 PHE cc_start: 0.7196 (m-80) cc_final: 0.6949 (m-80) REVERT: G 515 PHE cc_start: 0.7717 (m-80) cc_final: 0.7479 (m-80) REVERT: G 571 ASP cc_start: 0.7767 (t0) cc_final: 0.7407 (t0) REVERT: G 586 ASP cc_start: 0.7120 (t70) cc_final: 0.6902 (t0) REVERT: G 902 MET cc_start: 0.8822 (mmm) cc_final: 0.8431 (mmm) REVERT: G 904 TYR cc_start: 0.7036 (m-10) cc_final: 0.6767 (m-80) REVERT: G 1047 TYR cc_start: 0.8450 (m-80) cc_final: 0.8110 (m-10) REVERT: H 47 LEU cc_start: 0.5304 (tp) cc_final: 0.4899 (mt) outliers start: 51 outliers final: 31 residues processed: 232 average time/residue: 0.1413 time to fit residues: 56.4308 Evaluate side-chains 214 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 179 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 538 CYS Chi-restraints excluded: chain E residue 736 VAL Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain E residue 873 TYR Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 50 TRP Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain G residue 538 CYS Chi-restraints excluded: chain G residue 721 SER Chi-restraints excluded: chain G residue 731 MET Chi-restraints excluded: chain G residue 791 THR Chi-restraints excluded: chain G residue 869 MET Chi-restraints excluded: chain G residue 900 MET Chi-restraints excluded: chain G residue 1104 VAL Chi-restraints excluded: chain G residue 1116 THR Chi-restraints excluded: chain H residue 65 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 156 optimal weight: 20.0000 chunk 292 optimal weight: 0.0370 chunk 192 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 357 optimal weight: 5.9990 chunk 277 optimal weight: 30.0000 chunk 50 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 210 optimal weight: 0.9980 chunk 290 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 overall best weight: 1.0460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 GLN ** G1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.177709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.115694 restraints weight = 52365.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.118744 restraints weight = 31095.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.119278 restraints weight = 18695.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.120262 restraints weight = 15378.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.120387 restraints weight = 14266.499| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27105 Z= 0.130 Angle : 0.540 11.018 37077 Z= 0.272 Chirality : 0.045 0.219 4275 Planarity : 0.004 0.058 4848 Dihedral : 3.705 14.681 3900 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.86 % Allowed : 13.61 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.14), residues: 3627 helix: 2.18 (0.20), residues: 672 sheet: 0.68 (0.17), residues: 939 loop : -0.45 (0.14), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 815 TYR 0.025 0.001 TYR G 904 PHE 0.029 0.001 PHE A 592 TRP 0.022 0.001 TRP C 50 HIS 0.003 0.001 HIS E1064 Details of bonding type rmsd covalent geometry : bond 0.00296 (27057) covalent geometry : angle 0.53743 (36981) SS BOND : bond 0.00386 ( 48) SS BOND : angle 1.15183 ( 96) hydrogen bonds : bond 0.03839 ( 1186) hydrogen bonds : angle 5.23243 ( 3252) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 196 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: A 131 CYS cc_start: 0.2331 (m) cc_final: 0.1274 (m) REVERT: A 189 LEU cc_start: 0.8313 (tp) cc_final: 0.8030 (tp) REVERT: A 275 PHE cc_start: 0.7880 (m-80) cc_final: 0.7603 (m-10) REVERT: A 1047 TYR cc_start: 0.8654 (m-80) cc_final: 0.8424 (m-10) REVERT: C 2 MET cc_start: 0.5145 (mmt) cc_final: 0.4590 (mmt) REVERT: C 23 LYS cc_start: 0.6786 (mttp) cc_final: 0.6556 (ttpp) REVERT: C 46 GLU cc_start: 0.0344 (OUTLIER) cc_final: -0.0188 (pp20) REVERT: C 73 MET cc_start: -0.0421 (tpt) cc_final: -0.2620 (tmm) REVERT: C 108 MET cc_start: 0.2011 (mpp) cc_final: 0.0512 (mmt) REVERT: E 237 ARG cc_start: 0.7427 (ptt-90) cc_final: 0.7051 (ptt-90) REVERT: E 275 PHE cc_start: 0.7997 (m-80) cc_final: 0.7795 (m-10) REVERT: E 400 PHE cc_start: 0.7747 (p90) cc_final: 0.6785 (p90) REVERT: E 423 TYR cc_start: 0.6941 (t80) cc_final: 0.6441 (t80) REVERT: E 902 MET cc_start: 0.7973 (mmm) cc_final: 0.7443 (mmm) REVERT: E 904 TYR cc_start: 0.7642 (m-10) cc_final: 0.7388 (m-10) REVERT: E 1010 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.7320 (mp10) REVERT: F 2 MET cc_start: 0.0873 (ptt) cc_final: 0.0599 (mpp) REVERT: F 46 GLU cc_start: 0.2280 (OUTLIER) cc_final: 0.1473 (pm20) REVERT: F 65 GLU cc_start: 0.0650 (OUTLIER) cc_final: 0.0291 (pm20) REVERT: F 80 MET cc_start: 0.0862 (ppp) cc_final: -0.0276 (tmm) REVERT: G 48 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9078 (mt) REVERT: G 117 LEU cc_start: 0.8100 (mt) cc_final: 0.7745 (tp) REVERT: G 237 ARG cc_start: 0.7599 (mtm110) cc_final: 0.7074 (mtm180) REVERT: G 392 PHE cc_start: 0.7312 (m-80) cc_final: 0.7061 (m-80) REVERT: G 571 ASP cc_start: 0.7786 (t0) cc_final: 0.7429 (t0) REVERT: G 586 ASP cc_start: 0.7184 (t70) cc_final: 0.6941 (t0) REVERT: G 902 MET cc_start: 0.8731 (mmm) cc_final: 0.8356 (mmm) REVERT: G 904 TYR cc_start: 0.7024 (m-10) cc_final: 0.6702 (m-10) REVERT: G 998 THR cc_start: 0.8799 (m) cc_final: 0.8299 (p) REVERT: G 1047 TYR cc_start: 0.8392 (m-80) cc_final: 0.8080 (m-10) REVERT: H 47 LEU cc_start: 0.5341 (tp) cc_final: 0.4867 (mt) outliers start: 46 outliers final: 30 residues processed: 234 average time/residue: 0.1365 time to fit residues: 55.1370 Evaluate side-chains 220 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 185 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain E residue 538 CYS Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 736 VAL Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain E residue 1010 GLN Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 50 TRP Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 538 CYS Chi-restraints excluded: chain G residue 560 LEU Chi-restraints excluded: chain G residue 721 SER Chi-restraints excluded: chain G residue 791 THR Chi-restraints excluded: chain G residue 869 MET Chi-restraints excluded: chain G residue 900 MET Chi-restraints excluded: chain G residue 1104 VAL Chi-restraints excluded: chain G residue 1116 THR Chi-restraints excluded: chain I residue 87 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 13 optimal weight: 2.9990 chunk 356 optimal weight: 10.0000 chunk 138 optimal weight: 20.0000 chunk 171 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 361 optimal weight: 10.0000 chunk 351 optimal weight: 20.0000 chunk 111 optimal weight: 1.9990 chunk 299 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 187 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.175193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.117151 restraints weight = 52293.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.115571 restraints weight = 36103.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.116405 restraints weight = 24681.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.117106 restraints weight = 21369.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.117615 restraints weight = 17143.538| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 27105 Z= 0.208 Angle : 0.594 11.453 37077 Z= 0.303 Chirality : 0.047 0.244 4275 Planarity : 0.004 0.059 4848 Dihedral : 3.906 16.360 3900 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.66 % Allowed : 14.26 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.14), residues: 3627 helix: 2.02 (0.20), residues: 672 sheet: 0.56 (0.17), residues: 954 loop : -0.54 (0.14), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 815 TYR 0.025 0.001 TYR G 904 PHE 0.026 0.002 PHE E 92 TRP 0.020 0.001 TRP C 50 HIS 0.006 0.001 HIS E1064 Details of bonding type rmsd covalent geometry : bond 0.00487 (27057) covalent geometry : angle 0.59110 (36981) SS BOND : bond 0.00443 ( 48) SS BOND : angle 1.27219 ( 96) hydrogen bonds : bond 0.04304 ( 1186) hydrogen bonds : angle 5.39282 ( 3252) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 183 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: A 131 CYS cc_start: 0.2206 (m) cc_final: 0.1114 (m) REVERT: A 241 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.6755 (mm) REVERT: A 275 PHE cc_start: 0.7603 (m-80) cc_final: 0.7381 (m-10) REVERT: A 338 PHE cc_start: 0.8024 (m-10) cc_final: 0.7628 (m-80) REVERT: A 1047 TYR cc_start: 0.8680 (m-80) cc_final: 0.8423 (m-10) REVERT: C 2 MET cc_start: 0.5162 (mmt) cc_final: 0.4614 (mmt) REVERT: C 23 LYS cc_start: 0.6952 (mttp) cc_final: 0.6596 (ttpp) REVERT: C 73 MET cc_start: -0.0661 (tpt) cc_final: -0.2827 (tmm) REVERT: C 108 MET cc_start: 0.2312 (mpp) cc_final: 0.0571 (mmt) REVERT: E 237 ARG cc_start: 0.7478 (ptt-90) cc_final: 0.7033 (ptt-90) REVERT: E 275 PHE cc_start: 0.8095 (m-80) cc_final: 0.7887 (m-10) REVERT: E 400 PHE cc_start: 0.7799 (p90) cc_final: 0.6842 (p90) REVERT: E 423 TYR cc_start: 0.6626 (t80) cc_final: 0.6139 (t80) REVERT: E 675 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7605 (pp30) REVERT: E 820 ASP cc_start: 0.7917 (t70) cc_final: 0.7513 (t0) REVERT: E 902 MET cc_start: 0.8169 (mmm) cc_final: 0.7598 (mmm) REVERT: E 904 TYR cc_start: 0.7775 (m-10) cc_final: 0.7525 (m-10) REVERT: E 1010 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7229 (mp10) REVERT: F 46 GLU cc_start: 0.2135 (OUTLIER) cc_final: 0.1132 (pm20) REVERT: F 65 GLU cc_start: 0.1416 (OUTLIER) cc_final: 0.1014 (pm20) REVERT: F 80 MET cc_start: 0.1195 (ppp) cc_final: 0.0453 (tmm) REVERT: G 48 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9097 (mt) REVERT: G 237 ARG cc_start: 0.7638 (mtm110) cc_final: 0.7036 (mtm180) REVERT: G 392 PHE cc_start: 0.7079 (m-80) cc_final: 0.6719 (m-80) REVERT: G 571 ASP cc_start: 0.7910 (t0) cc_final: 0.7545 (t0) REVERT: G 902 MET cc_start: 0.8662 (mmm) cc_final: 0.8288 (mmm) REVERT: G 998 THR cc_start: 0.8877 (m) cc_final: 0.8362 (p) REVERT: G 1047 TYR cc_start: 0.8450 (m-80) cc_final: 0.8111 (m-10) REVERT: H 47 LEU cc_start: 0.5020 (tp) cc_final: 0.4510 (mt) outliers start: 41 outliers final: 31 residues processed: 217 average time/residue: 0.1363 time to fit residues: 50.8629 Evaluate side-chains 215 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 178 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain E residue 538 CYS Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 675 GLN Chi-restraints excluded: chain E residue 736 VAL Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain E residue 873 TYR Chi-restraints excluded: chain E residue 1010 GLN Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 50 TRP Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 538 CYS Chi-restraints excluded: chain G residue 721 SER Chi-restraints excluded: chain G residue 791 THR Chi-restraints excluded: chain G residue 869 MET Chi-restraints excluded: chain G residue 900 MET Chi-restraints excluded: chain G residue 1104 VAL Chi-restraints excluded: chain G residue 1116 THR Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain I residue 87 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 83 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 293 optimal weight: 0.5980 chunk 98 optimal weight: 0.0570 chunk 254 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 chunk 301 optimal weight: 0.6980 chunk 327 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 157 optimal weight: 30.0000 chunk 355 optimal weight: 20.0000 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 901 GLN G 955 ASN G1010 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.177001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.114447 restraints weight = 52313.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.119021 restraints weight = 24787.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.120231 restraints weight = 13417.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.120477 restraints weight = 11593.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.120756 restraints weight = 10680.213| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 27105 Z= 0.117 Angle : 0.545 12.265 37077 Z= 0.272 Chirality : 0.045 0.245 4275 Planarity : 0.004 0.057 4848 Dihedral : 3.662 14.892 3900 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.26 % Allowed : 14.90 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.14), residues: 3627 helix: 2.21 (0.20), residues: 672 sheet: 0.63 (0.17), residues: 969 loop : -0.46 (0.14), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 815 TYR 0.045 0.001 TYR G 904 PHE 0.024 0.001 PHE E 92 TRP 0.024 0.001 TRP C 50 HIS 0.002 0.000 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00266 (27057) covalent geometry : angle 0.54231 (36981) SS BOND : bond 0.00340 ( 48) SS BOND : angle 1.17467 ( 96) hydrogen bonds : bond 0.03697 ( 1186) hydrogen bonds : angle 5.13485 ( 3252) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 187 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 CYS cc_start: 0.1838 (m) cc_final: 0.0803 (m) REVERT: A 241 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.6682 (mm) REVERT: A 338 PHE cc_start: 0.8026 (m-10) cc_final: 0.7605 (m-80) REVERT: A 1047 TYR cc_start: 0.8639 (m-80) cc_final: 0.8407 (m-10) REVERT: C 2 MET cc_start: 0.5160 (mmt) cc_final: 0.4624 (mmt) REVERT: C 23 LYS cc_start: 0.6804 (mttp) cc_final: 0.6556 (ttpp) REVERT: C 73 MET cc_start: -0.0582 (tpt) cc_final: -0.2563 (tmm) REVERT: C 108 MET cc_start: 0.2079 (mpp) cc_final: 0.0497 (mmt) REVERT: E 237 ARG cc_start: 0.7437 (ptt-90) cc_final: 0.7115 (ptt-90) REVERT: E 275 PHE cc_start: 0.7919 (m-80) cc_final: 0.7637 (m-10) REVERT: E 400 PHE cc_start: 0.7754 (p90) cc_final: 0.6812 (p90) REVERT: E 423 TYR cc_start: 0.6687 (t80) cc_final: 0.6187 (t80) REVERT: E 820 ASP cc_start: 0.7753 (t70) cc_final: 0.7337 (t0) REVERT: E 902 MET cc_start: 0.8054 (mmm) cc_final: 0.7586 (mmm) REVERT: E 904 TYR cc_start: 0.7858 (m-10) cc_final: 0.7578 (m-10) REVERT: E 1010 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7323 (mp10) REVERT: F 46 GLU cc_start: 0.2127 (OUTLIER) cc_final: 0.1174 (pm20) REVERT: F 65 GLU cc_start: 0.1388 (OUTLIER) cc_final: 0.0987 (pm20) REVERT: G 48 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9108 (mt) REVERT: G 237 ARG cc_start: 0.7628 (mtm110) cc_final: 0.7109 (mtm180) REVERT: G 392 PHE cc_start: 0.7118 (m-80) cc_final: 0.6739 (m-10) REVERT: G 571 ASP cc_start: 0.7845 (t70) cc_final: 0.7499 (t70) REVERT: G 586 ASP cc_start: 0.6784 (t70) cc_final: 0.6526 (t0) REVERT: G 902 MET cc_start: 0.8607 (mmm) cc_final: 0.8206 (mmm) REVERT: G 998 THR cc_start: 0.8776 (m) cc_final: 0.8287 (p) REVERT: G 1047 TYR cc_start: 0.8415 (m-80) cc_final: 0.8094 (m-10) REVERT: H 47 LEU cc_start: 0.5297 (tp) cc_final: 0.4663 (mt) outliers start: 31 outliers final: 24 residues processed: 212 average time/residue: 0.1426 time to fit residues: 51.7515 Evaluate side-chains 208 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 179 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain E residue 538 CYS Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain E residue 1010 GLN Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 50 TRP Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 538 CYS Chi-restraints excluded: chain G residue 791 THR Chi-restraints excluded: chain G residue 869 MET Chi-restraints excluded: chain G residue 900 MET Chi-restraints excluded: chain G residue 1104 VAL Chi-restraints excluded: chain G residue 1116 THR Chi-restraints excluded: chain I residue 87 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 162 optimal weight: 30.0000 chunk 309 optimal weight: 0.0270 chunk 85 optimal weight: 0.9990 chunk 185 optimal weight: 3.9990 chunk 261 optimal weight: 0.6980 chunk 277 optimal weight: 30.0000 chunk 173 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 247 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1010 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.177883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.114863 restraints weight = 52007.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.119175 restraints weight = 24705.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.120559 restraints weight = 14370.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.120999 restraints weight = 12748.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.122186 restraints weight = 10436.998| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 27105 Z= 0.107 Angle : 0.538 13.015 37077 Z= 0.267 Chirality : 0.045 0.232 4275 Planarity : 0.004 0.053 4848 Dihedral : 3.559 14.923 3900 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.46 % Allowed : 14.66 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.14), residues: 3627 helix: 2.28 (0.20), residues: 672 sheet: 0.71 (0.17), residues: 969 loop : -0.42 (0.14), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 815 TYR 0.041 0.001 TYR G 904 PHE 0.026 0.001 PHE G 168 TRP 0.025 0.001 TRP C 50 HIS 0.001 0.000 HIS G1088 Details of bonding type rmsd covalent geometry : bond 0.00240 (27057) covalent geometry : angle 0.53636 (36981) SS BOND : bond 0.00312 ( 48) SS BOND : angle 1.07729 ( 96) hydrogen bonds : bond 0.03534 ( 1186) hydrogen bonds : angle 5.01854 ( 3252) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4524.48 seconds wall clock time: 78 minutes 29.24 seconds (4709.24 seconds total)